The analysis of genetic data for the purpose of identifying conservation priorities may draw from one or more biological subdisciplines depending on the specific questions at hand. As such the proliferation of different methods for analyzing and interpreting genetic data in such fields as molecular systematics and population genetics has been paralleled in conservation. We explore the respective realms of utility for these fields and approaches by discussing the juxtaposition of analyses of character distributions with more commonly and often casually used tree-based analyses. In so doing, the biological, philosophical, and methodological convergences and conflicts of these frameworks are explicated using empirical examples, as are some of the areas of overlap among and disagreement over phylogenetic species criteria and other alternatives. In the arena of conservation biology, systematics and population genetics complement one another and may facilitate the identification of management units at intraspecific levels, or more properly intra-nominal levels when species boundaries are defined according to the biological species concept. The comparison of these methods heightens the contrast between graphical representation of reciprocal monophyly at traditionally intra-nominal levels and the identification of groupings actually supported by fixed diagnostic characters as prospective conservation tools. Since character fixation is widely regarded as an early stage in the "ontogeny" of species evolution, character-based approaches to delineating management units provide a suitable framework from within which to explore the complementarity of the two major subdisciplines of evolutionary biology and their respective contributions to conservation.